There are endo-type and exo-type ribonucleases (RNA-degrading enzymes). Their substrate specificities are diverse, and they are involved in complicated physiological activities. Enzymes such as ribonuclease T1, ribonuclease T2, ribonuclease H, ribonuclease P, ribonuclease I, ribonuclease II, ribonuclease III, ribonuclease IV, ribonuclease L are known to have ribonuclease activities.
Ribonuclease H (hereinafter also referred to as RNase H) was first isolated from calf thymus by W. H. Stein and P. Hausen in 1969. RNase Hs are currently classified into cellular RNase Hs and viral RNase Hs. The cellular RNase Hs are widely present in eukaryotes such as various animal cells and yeasts and prokaryotes such as Escherichia coli, whereas the viral RNase Hs are present in RNA tumor viruses. Several kinds of RNase H activities are present in a cell. They require divalent metal ions such as Mg2+ and Mn2+.
An RNase H from Escherichia coli is a hydrolase that consists of 155 amino acids, has a molecular weight of about 17 kDa and has a substrate specificity of specifically cleaving only the RNA strand in a DNA-RNA hybrid in an endo-type manner. The resulting oligomer has a phosphate group at the 5′ end and a hydroxyl group at the 3′ end.
RNase HI and RNase HII have been identified as RNase Hs from E. coli. It has been shown that RNase HI has the following physiological functions in the replication of the Col E1 plasmid: 1) it degrades RNAs bound to portions other than the normal replication origin to ensure the normal replication origin; and 2) it synthesizes an RNA primer specific for the normal replication origin. On the other hand, the function of RNase HII remains unknown.
RNase Hs have uses as exemplified below based on the substrate specificities, and attention is paid to RNase Hs as very valuable enzymes:
1) removal of template mRNA upon cDNA cloning;
2) removal of poly(A) region in mRNA; and
3) fragmentation of RNA.
It is considered that RNase H increasingly becomes important with the development of genetic engineering. However, the expression level of this enzyme in E. coli is quite low. Then, production of this enzyme using recombinant DNA techniques has been attempted. RNase Hs produced using recombinant DNA techniques are now supplied from BRL, Amersham Pharmacia Biotech, Takara Bio and the like.
These commercially available recombinant RNase Hs are produced using Escherichia coli as a host (Kanaya et al., The Journal of Biological Chemistry, 264:11546-11549 (1989)). A method of producing an RNase H from a thermophile, which is much more stable than RNase H from E. coli, using E. coli has been reported (Kanaya et al., Dai 2 Kai Nippon Tanpakukougakukai Nenkai Program/Abstract (1990) pp. 69; Japanese Patent No. 2533671). However, the enzymatic activity of the RNase H from a thermophile produced using E. coli was lower than that of RNase H from E. coli. 
As described above, only thermostable RNase Hs whose productivities and enzymatic activities are lower than those of RNase H from E. coli are available. Thus, development of a thermostable RNase H whose productivity and enzymatic activity are equivalent to or more than those of the RNase H from E. coli has been desired for expanding the uses of RNase H.
Then, RNase Hs having varying thermostabilities have been cloned in order to solve the above-mentioned problems. Examples thereof include RNase Hs derived from Bacillus caldotenax, Pyrococcus furriosus, Thermotoga maritima, Archaeoglobus fulgidus, Thermococcus litoralis, Thermococcus celer and Pyrococcus horikoshii as described in WO 02/22831.
Further examples include RNase Hs derived from Thermus thermophilus (Nucleic Acids Research, Vol. 19, No. 16, p 4443-4449 (1991); U.S. Pat. No. 5,268,289), Pyrococcus furiosus (U.S. Pat. No. 5,610,066), Pyrococcus sp. KOD1 (JP-A 11-32772) and Archaeoglobus fulgidus (Journal of Molecular Biology, Vol. 307, p 541-556 (2001)).
However, there have been many problems to be improved concerning these RNase Hs such as low thermostability, decreased activity on a DNA-RNA hybrid having short RNA strand and low specific activity. Then, development of further thermostable RNase H having distinct substrate specificity or mode of action has been desired to meet the importance of RNase H which is considered to be increased more and more with the development of genetic engineering.